Alex Ball: CSI Banteng - using genetics in conservation

Alex Ball, Photo courtesy of Alex Ball

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As animals all over the world struggle with the impacts of human activity, such as shrinking habitats, climate change and wildlife trafficking, conservationists are doing their best to save them. To find out more about how genetics is being put to work to understand and preserve species in a changing world, I caught up with Alex Ball from the Royal Zoological Society of Scotland’s Wild Genes programme, based at Edinburgh Zoo.

Alex: So there's three main themes that we work on within the wild genes lab. One of them is using genetics to look at the origin of illegally traded wildlife products or individual animals as well, If we can get samples on, just to work out potentially where captive populations have come from in the wild and where they may have been poached from as well in the case of the illegal trade. We also look at population structure of remaining threatened and fragmented populations and potential gene flow between them to determine if there is still movement between these populations, wherever we may need to set up corridors, for example, between them. 

Alex: And then another key part, which many people associate with zoos, is looking at captive breeding programs and the relatedness between individuals trying to avoid inbreeding within captive populations. And so although people often jump to that when they think about zoos and genetic conservation, it is actually quite a small part of our work. Because a lot of programs, especially within the European association of zoos and aquaria, have very good management and stud books and they do record that information quite readily. So we don't need to use genetics as much as people do think for that side of things.

Kat: So let's start with the area of illegal wildlife and the movement of animals. What sort of tools and techniques are you actually using to track the illegal wildlife trade? How does that actually work? The CSI ivory?

Alex: Yeah. So one of the projects we do work with is elephant ivory, and there's actually quite a big database that has been built up, surrounding elephant populations within Africa and a huge number of samples that have been identified and located in different geographic regions. However often how it starts is with conservation practitioners on the ground. They come to us with a case potentially in the country. So for example, we got a request about a Banteng that had been poached and it had been found in a village in a remote part of Cambodia. So Banteng is a species of cattle and an endangered species of cow that is protected. And what they wanted to know was who had potentially poached this individual and they'd located two different parts of the Banteng, one was the horn and one was the carcass and they knew who had the horn, but the carcass had been left in the forest and they were like, is this from the same individual? Can we trace back the person who has this horn to this carcass?

Alex: And really at that point, there's a lot of work that needs to be done. We hadn't worked with Banteng before. It was a completely new species, a novel species, we hadn't developed markers or anything. And so we really couldn't take it very far, but what we try and do is once we have questions like that coming in, we then try and get those tools in place and work with different NGOs on the ground, within the country to potentially, if that question comes up again, we then have the tools to do it. Because basically we need a lot of reference samples, we need a big database of samples from that species and closely related species to be able to design the markers and then answer questions like that, that are really practical and on the ground and that could help with enforcement and legislation in the countries.

Kat: Did you ever actually find out if it was the same Banteng?

Alex: I'm afraid not. We didn't pursue that one just because one of our main focuses in that country is on the ivory trade, and so we really put a lot of effort into trying to sample the Asian elephant populations and that's already a big project within the country. And so we actually haven't pursued that case and that sample. And they wanted a really fast turnaround, as you can imagine, potentially go into a court case. It wasn't at that point, they just wanted to see if we could do it initially.

Kat: And so moving from Bantengs and ivory and illegally traded animals, how else is the genetics work that's going on helping to understand populations that are still alive and, haven't been illegally poached, what kind of work can you do? What kind of things can you understand about wild populations of animals using genetic techniques?

Alex: Yeah, so we do look at general ecological questions as well that may not be directly linked to conservation or the link is not completely obvious. So for example, we do look at diet. So we use genetic metabarcoding techniques to look at the diet of tigers in Nepal is one project we've done.

Kat: This is poop, isn't it? This is poop analysis. Metagenomics is poop.

Alex: Yeah. So we sort of have a nickname. We're like the shit geneticists. Oops, sorry. I shouldn't probably say that.

Kat: I think we'll let that one go. So you're, you're basically looking at tiger poo to see what they're eating, to see where, where they've been having their dinner.

Alex: Yes. So in terms of that project, we are trying to work out what prey items tigers are relying on in the wild, in the wild populations, and that it gives us an indication of what prey items are there, but also their prey item preference. If you can combine it with field surveys for different areas. But another key thing is human wildlife conflict with tigers in Nepal. And there's potentially, they do prey on livestock and that can lead to retaliation by villages and human communities, in neighbouring areas to the tigers. And so one of the reasons we developed this protocol using captive tiger poo from the Edinburgh Zoo tigers was to inform, villages or inform the wider community, where the tigers in that region are feeding on agricultural livestock. So for example, goats and Buffalo that are basically free range around these villages, they don't really keep them in pens like people would over in Europe and the UK.

Kat: Oh wow. So the villages are saying, I think the tigers are stealing my goats and you can say, Hmm, they're not eating goats actually. So not your goats.

Alex: Yes, exactly. Or it can be the other way round where it hasn't been picked up on yet, but we can sort of work out that there might be a hotspot where an individual is targeting agricultural livestock in the villages and then teams can go out and basically help advise the villages on different mitigation techniques that they could put in place. Or that tiger, If we can identify that it's an individual tiger that actually has that preference, can potentially be moved to an area without those agricultural livestocks close by.

Kat: All right. So if it's got a predilection for goat, you're like, let's move it away from the goats.

Alex: Yeah. So we're working with lots of NGOs in the country that that's their task and their aim to work on that side of it. But we provide the underlying genetic data that lets them know what the tigers have eaten.

Kat: And moving from what the tigers like to eat and the wild populations in general, obviously keeping these populations relies on having a habitat and also tigers falling in love and making more tiger babies. So how can we understand what's happening with the populations? How are the populations in the wild doing? How do you kind of map that stuff?

Alex: Yeah. So to get an idea of how successful the populations are doing in the wild there's various techniques you can use. Obviously we look at genetic diversity, just baseline genetic diversity across a genome so that we can compare between different populations. We also look back in time, so historically, to compare what the genetic diversity in present day populations, how it compares to those past populations.Have the declines led to a loss of genetic diversity and bottlenecks in certain populations? Can we identify which ones have undergone more serious declines than others? We also look at gene flow between populations. So are they still connected?

Alex: So for example, we have a population of Northern Rockhopper penguins. So these breed in Southern Atlantic and Indian oceans, and there's two sort of main breeding populations, one on Gough Island and Tristan Da Cunha and islands in the middle of the Atlantic and then others in the Southern Indian ocean. And it's really not known whether there's movement between those breeding colonies, can disease be transmitted between those colonies at all? Because some are facing serious declines because of various introduced disease. So can we use genetics to see whether there is potential of that transfer of the disease or whether if one population went extinct, would that affect in any way these populations on these other islands, because there is transfer between them or not.

Kat: So do you have to go to these islands in the middle of nowhere and catch penguins?

Alex: So I'm afraid I don't do that, I'm very much lab based.

Kat: Bummer.

Alex: I know, but we get samples from all over the world and we work with researchers at the British Antarctic survey, for example, the RSPB who do go out annually to these really remote locations. And actually we do have a vet who is heading out, so from Edinburgh Zoo, one of our vets is heading out this weekend to Gough Island to collect samples and do some work there for another project with the RSPB

Kat: Fantastic. But then it's not just exotic animals, tigers and Antarctic penguins. I know that you're also working with animals that are much closer to home because we still have endangered populations here in the UK. So what's some of the projects that are going on there.

Alex: Yes, we do have quite a suite of native species projects that we focus on. One of the key ones that we have input via genetics is on the Wild Cats project. So it's the last remaining wild felid that we have in this country and the last remaining populations are within Scotland and have been for the last few hundred years. So they've really just been clinging on in this country and so it's a really big effort to try and protect these few remaining wild cats. We also work on lesser known species such as the Pine Hoverfly, which is an endangered insect in the Cairngorms and species like the Capercaillie as well, which might be more well known to listeners. So we work with the RSPB and Cairngorms National Park Authority on trying to protect the few remaining birds. They've been fluctuating around a thousand individuals left in the wild, so it's not many at all.

Kat: Oh Wow. It it's interesting isn't it with conservation because obviously you know that the Panda is an icon of conservation, wild cats - very cute, Capercaillies - iconic birds, Pine Hoverflies - not very sexy. Is it hard to persuade people that it's really important to care about these kind of overlooked smaller or less sexy and cuddly species when it comes to understanding the populations and conserving them?

Alex: Yeah, this is a really key part of our work and a really big part of our engagement work as well, because the Royal Zoological Society of Scotland also owns Edinburgh Zoo and Highland Wildlife Park It really gives us an opportunity to communicate with the public about these lesser known species because they come to see those big, iconic species like you mentioned, the pandas, but at the same time we can then inform them about these ones that very little is known about even within the scientific community. But the Pine Hoverflies they've hardly been seen in the wild for the last couple of decades, and so it's really, really key that we get a better understanding of their declines and how few there are remaining and what we can do, being part of a zoo and captive breeding programs, we have instigated some of the breeding so we can release more of these individuals back into the wild and help boost those dwindling populations there.

Kat: Well, as someone who doesn't particularly like insects, I understand it's important, but let's talk a bit more about this idea of captive breeding. So I've been to London zoo to meet the tigers there and the person who looks after the tigers and the stud book and it's like she's like the Cilla Black of tigers. It's all the matings of the Sumatran Tigers and you know where they are all over the world, and who's been on a date, so to speak, and it's just fantastically detailed work that has to go on to preserve these species and to make sure that there is enough difference that these animals can survive what a changing world is going to throw at them, I guess.

Alex: That's the key reason we focus on genetic diversity, is because that is the only way that a species is going to be able to adapt with that underlying diversity that is there. We don't know which parts of that diversity are going to be important for those species in the future. So we have to maintain as much of it as we can as possible in this population. So that's really the main goal when you have captive populations and even in wild populations with the constantly changing climates and the different persecution and different effects that animals are facing in the wild now it's really gonna rely on them being able to adapt to it.

Kat: I think that's always the thing with evolution. People say, "Oh well let's look at the genes and find out what they've got." You don't know what's important. It's just that this diversity is fuel for evolution and somehow species we've got to try and MacGyver their way out of what's happening to them and if they don't have enough genetic fuel in their tank, they're really going to struggle.

Alex: Yeah. That is the really fundamental point. That is really key that we don't know what Genetic diversity is important. We don't know what genes they're going to need in the future and what little mutations or changes are going to be the important ones in the future. So we just need to keep as much of it as we can, as possible.

Kat: Alex Ball, from the Royal Zoological Society of Scotland’s Wild Genes programme.